documentation updates

Author: JWiley

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: multilevelTools
 Title: Multilevel and Mixed Effects Model Diagnostics and Effect Sizes
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: 
     person(given = "Joshua F.",
            family = "Wiley",

NEWS.md

@@ -1,3 +1,8 @@
+# multilevelTools 0.2.1
+
+## Changes
+* Improved documentation links to functions in other packages.
+
 # multilevelTools 0.2.0
 
 ## New Features

R/descriptives.R

@@ -265,8 +265,8 @@ meanDeviations <- function(x, na.rm = TRUE) {
 #' @param na.function A character string giving the name of the function
 #'   to use to address any missing data.  Functions come from the
 #'   \pkg{zoo} package, and must be one of:
-#'   \dQuote{na.approx}, \dQuote{na.spline}, \dQuote{na.locf}.
-#' @param ... Additional arguments passed to \code{zoo}.
+#'   \code{\link[zoo]{na.approx}}, \code{\link[zoo]{na.spline}}, \code{\link[zoo]{na.locf}}.
+#' @param ... Additional arguments passed on.
 #' @return A data.table of the estimated autocorrelations by ID and lag
 #' @keywords multivariate
 #' @importFrom data.table copy is.data.table as.data.table data.table

R/diagnostics.R

@@ -7,15 +7,15 @@ if(getRversion() >= "2.15.1") {
 
 #' residualDiagnostics methods for merMod objects
 #'
-#' @param object An object with class \code{merMod}. Currently only
-#'   \code{lmer()} models are supported.
+#' @param object An object with class \code{\link[lme4]{merMod-class}}. Currently only
+#'   \code{\link[lme4]{lmer}} models are supported.
 #' @param ev.perc The extreme value percentile to use. Defaults to
 #'   .001.
 #' @param robust A logical value, whether to use robust estimates or not.
 #'   Defaults to \code{FALSE}.
 #' @param distr A character string specifying the assumed distribution.
 #'   Currently \dQuote{normal}, but may expand in the future if
-#'   \code{glmer()} models are supported.
+#'   \code{\link[lme4]{glmer}} models are supported.
 #' @param standardized A logical value whether to use standardized
 #'   residual values or not. Defaults to \code{TRUE}.
 #' @param cut An integer, how many unique predicted values
@@ -132,10 +132,10 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c(".SD", "isEV", "Original
 #' modelDiagnostics method for merMod objects
 #'
 #' This function creates a number of diagnostics
-#' for \code{merMod} models.
+#' for \code{\link[lme4]{merMod-class}} models.
 #'
-#' @param object A fitted model object, either of class merMod from
-#'   the lme4 package or merModLmerTest from the lmerTest package.
+#' @param object A fitted model object, either of \code{\link[lme4]{merMod-class}} from
+#'   the \pkg{lme4} package or merModLmerTest from the \pkg{lmerTest} package.
 #' @param ev.perc A real number between 0 and 1 indicating the
 #'   proportion of the theoretical distribution beyond which
 #'   values are considered extreme values (possible outliers).
@@ -149,7 +149,7 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c(".SD", "isEV", "Original
 #'   Defaults to \code{TRUE} generally where possible but may depend on
 #'   method.
 #' @param ... Additional arguments, passed to \code{\link[JWileymisc]{residualDiagnostics}}.
-#' @return A logical (\code{is.modelDiagnostics}) or
+#' @return A logical \code{\link[JWileymisc]{is.modelDiagnostics}} or
 #'   a modelDiagnostics object (list) for
 #'   \code{\link[JWileymisc]{as.modelDiagnostics}} and 
 #'   \code{\link[JWileymisc]{modelDiagnostics}}.
@@ -263,9 +263,9 @@ modelDiagnostics.merMod <- function(object, ev.perc = .001,
   as.modelDiagnostics(out)
 }
 
-#' residualDiagnostics methods for lme objects
+#' residualDiagnostics methods for \code{\link[nlme]{lme}} objects
 #'
-#' @param object An object with class \code{lme}.
+#' @param object An object from \code{\link[nlme]{lme}}.
 #' @param ev.perc The extreme value percentile to use. Defaults to
 #'   .001.
 #' @param robust A logical value, whether to use robust estimates or not.
@@ -389,9 +389,9 @@ residualDiagnostics.lme <- function(object, ev.perc = .001,
 #' modelDiagnostics method for lme objects
 #'
 #' This function creates a number of diagnostics
-#' for \code{lme} models.
+#' for \code{\link[nlme]{lme}} models.
 #'
-#' @param object A fitted model object  of class lme.
+#' @param object A fitted model object from \code{\link[nlme]{lme}}.
 #' @param ev.perc A real number between 0 and 1 indicating the
 #'   proportion of the theoretical distribution beyond which
 #'   values are considered extreme values (possible outliers).
@@ -531,4 +531,3 @@ modelDiagnostics.lme <- function(object, ev.perc = .001,
 
   as.modelDiagnostics(out)
 }
-

R/models.R

@@ -10,7 +10,7 @@
 #' @param id A character string giving the name of the variable that
 #'  indicates which rows of the dataset belong to the same person
 #'  or group for the multilevel analysis.
-#' @param data A data table or data frame to be used for analysis.
+#' @param data A \code{data.table} or \code{data.frame} to be used for analysis.
 #' @param savemodel A logical value indicating whether the underlying model
 #'  should be saved and returned. Defaults to \code{FALSE}.
 #' @return a list with two elements, the first, \dQuote{Results} contains the
@@ -23,7 +23,6 @@
 #' @export
 #' @importFrom lavaan sem parameterEstimates
 #' @examples
-#'
 #'   data(aces_daily, package = "JWileymisc")
 #'   omegaSEM(
 #'     items = c("COPEPrb", "COPEPrc", "COPEExp"),
@@ -316,8 +315,8 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c("Estimator", "N_Groups",
 #' This function provides fit statistics and effect sizes for
 #' model comparisons.  The models must be nested.
 #'
-#' @param model1 A model estimated by \code{lmer}.
-#' @param model2 A model estimated by \code{lmer}.
+#' @param model1 A model estimated by \code{\link[lme4]{lmer}}.
+#' @param model2 A model estimated by \code{\link[lme4]{lmer}}.
 #' @param ... Additional arguments, not currently used but included to match generic.
 #' @return a data table with the fit indices for each model
 #' and comparing models to each other.
@@ -429,13 +428,13 @@ if(getRversion() >= "2.15.1") utils::globalVariables(c("var1", "var2", "sdcor",
 
 #' estimate detailed results per variable and effect sizes for both fixed and random effects from lmer models
 #'
-#' This function extends the current \code{drop1} method for
+#' This function extends the current \code{\link[stats]{drop1}} method for
 #' \code{merMod} class objects from the lme4 package. Where
 #' the default method to be able to drop both fixed and random
 #' effects at once.
 #'
-#' At the moment, the function is aimed to \code{lmer} models
-#' and has very few features for \code{glmer} or \code{nlmer}
+#' At the moment, the function is aimed to \code{\link[lme4]{lmer}} models
+#' and has very few features for \code{\link[lme4]{glmer}} or \code{\link[lme4]{nlmer}}
 #' models. The primary motivation was to provide a way to
 #' provide an overall test of whether a variable
 #' \dQuote{matters}.  In multilevel data, a variable may be
@@ -453,9 +452,9 @@ if(getRversion() >= "2.15.1") utils::globalVariables(c("var1", "var2", "sdcor",
 #' mixed effects models do not accomodate all types of models. For example,
 #' if a model includes only a random slope with no random intercept,
 #' if the random slope was dropped, there would be no more random effects,
-#' and at that point, \code{lmer} or \code{glmer} will not run the model.
+#' and at that point, \code{\link[lme4]{lmer}} or \code{\link[lme4]{glmer}} will not run the model.
 #' It is theoretically possible to instead fit the model using
-#' \code{lm} or \code{glm} but this becomes more complex for certain
+#' \code{\link[stats]{lm}} or \code{\link[stats]{glm}} but this becomes more complex for certain
 #' model comparisons and calculations and is not currently implemented.
 #' Marginal and conditional R2 values are calculated for each term,
 #' and these are used also to calculate something akin to an
@@ -474,12 +473,12 @@ if(getRversion() >= "2.15.1") utils::globalVariables(c("var1", "var2", "sdcor",
 #' main effect but keeping the interaction term, so present
 #' and interpret these with caution.
 #'
-#' @param object A \code{merMod} class object, the fitted result of
-#'   \code{lmer}.
+#' @param object A \code{link[lme4]{merMod-class}} object, the fitted result of
+#'   \code{\link[lme4]{lmer}}.
 #' @param method A character vector indicating the types of confidence
 #'   intervals to calculate. One of \dQuote{Wald}, \dQuote{profile}, or
 #'   \dQuote{boot}.
-#' @param control A \code{lmerControl()} results used to control how
+#' @param control A \code{\link[lme4]{lmerControl}} results used to control how
 #'   models are estimated when updating.
 #' @param ... Additional arguments passed to \code{confint}
 #' @importFrom JWileymisc modelTest as.na as.modelTest
@@ -495,7 +494,7 @@ if(getRversion() >= "2.15.1") utils::globalVariables(c("var1", "var2", "sdcor",
 #' ## these examples are slow to run
 #' library(JWileymisc)
 #' m1 <- lme4::lmer(extra ~ group + (1 | ID),
-#' data = sleep, REML=FALSE)
+#'   data = sleep, REML = FALSE)
 #' modelTest(m1)
 #'
 #' \donttest{
@@ -748,7 +747,7 @@ modelTest.merMod <- function(object, method = c("Wald", "profile", "boot"), cont
 #'
 #' Currently only linear mixed effects models are allowed.
 #'
-#' @param formula A \code{character} string giving the \code{lmer()} formula
+#' @param formula A \code{character} string giving the \code{\link[lme4]{lmer}} formula
 #'   to use as a base. The variable to be tested with lags gets added as fixed effects
 #'   only to this, currently.
 #' @param lagvar A \code{character} string giving the name of the variable to test lags for.

R/plotting.R

@@ -3,12 +3,12 @@
 ## clear R CMD CHECK notes
 if(getRversion() >= "2.15.1")  utils::globalVariables(c("EffectType", "OriginalOrder"))
 
-#' Plot Diagnostics for an lmer model
+#' Plot Diagnostics for an \code{\link[lme4]{lmer}} model
 #'
 #' This function creates a number of diagnostic plots
-#' from lmer models.
+#' from \code{\link[lme4]{lmer}} models.
 #'
-#' @param x A fitted model object from \code{lmer()}.
+#' @param x A fitted model object from \code{\link[lme4]{lmer}}.
 #' @param y Included to match the generic. Not used.
 #' @param plot A logical value whether or not to plot the results or
 #'   simply return the graphical objects.
@@ -88,12 +88,12 @@ plot.modelDiagnostics.merMod <- function(x, y, plot = TRUE, ask = TRUE, ncol = 1
 }
 
 
-#' Plot Diagnostics for an lme model
+#' Plot Diagnostics for an \code{\link[nlme]{lme}} model
 #'
 #' This function creates a number of diagnostic plots
 #' from lme models.
 #'
-#' @param x A fitted model object from \code{lme()}.
+#' @param x A fitted model object from \code{\link[nlme]{lme}}.
 #' @param y Included to match the generic. Not used.
 #' @param plot A logical value whether or not to plot the results or
 #'   simply return the graphical objects.

R/ranef.r

@@ -42,11 +42,11 @@ if (getRversion() >= "2.15.1")  utils::globalVariables(c("iteration"))
 if (getRversion() >= "2.15.1")  utils::globalVariables(c("e", ".x", "A", "B",
   "interceptA", "interceptB", "sigmaA", "sigmaB", "x", "y", "vars"))
 
-#' Create data and plots for brms random effect models
+#' Create data and plots for \code{\link[brms]{brm}} random effect models
 #' 
-#' @param object a \code{brmsfit} objectx
+#' @param object a \code{\link[brms]{brmsfit-class}} object
 #' @param usevars a character vector of random effects to plot
-#' @param newdata a data.table object with the data used to generate the random effects, this is used as an anchor for the random intercepts so they have a meaningful 0 point
+#' @param newdata a \code{data.table} object with the data used to generate the random effects, this is used as an anchor for the random intercepts so they have a meaningful 0 point
 #' @param idvar a character string specifying the grouping variable name for the random effects 
 #' @param CI a numeric value between 0 and 1 specifying the interval to use. Defaults to 0.95.
 #' @param robust a logical value indicating whether to use robust estimates or not. Defaults to FALSE.

R/styler.R

@@ -21,7 +21,7 @@ if(getRversion() >= "2.15.1") {
 #'   change all parts of the output (which default to 2 decimals per
 #'   APA style).
 #' @param pcontrol A list controlling how p values are formatted.
-#' @param ... Additional arguments passed to \code{confint}. Notably
+#' @param ... Additional arguments passed to \code{\link[stats]{confint}}. Notably
 #'   \code{nsim} and \code{boot.type} if the bootstrap method is used.
 #' @return a data table of character data
 #' @keywords misc